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gspread-pandas
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public |
A package to easily open an instance of a Google spreadsheet and interact with worksheets through Pandas DataFrames.
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2025-04-22 |
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cmake_format
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public |
Can format your listfiles so they don't look like crap
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2025-04-22 |
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r-leiden
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public |
Implements the 'Python leidenalg' module to be called in R. Enables clustering using the leiden algorithm for partition a graph into communities. See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg> Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
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2025-04-22 |
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sphinxdft
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public |
S/PHI/nX is a C++ library for materials simulation, mostly electronic-structure theory
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2025-04-22 |
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flask-talisman
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public |
HTTP security headers for Flask
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2025-04-22 |
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px-proxy
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public |
An HTTP proxy server to automatically authenticate through an NTLM proxy
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2025-04-22 |
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pybloom_live
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public |
Scalable Bloom Filter implemented in Python
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2025-04-22 |
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codespell
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public |
Fix common misspellings in text files, usually source code.
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2025-04-22 |
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ann
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public |
ANN: A Library for Approximate Nearest Neighbor Searching
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2025-04-22 |
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elephas
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public |
Deep learning on Spark with Keras
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2025-04-22 |
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r-breakaway
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public |
Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa, and betta_random() permits random effects modelling.
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2025-04-22 |
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r-blockfest
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public |
An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
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2025-04-22 |
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r-airr
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public |
Schema definitions and read, write and validation tools for data formatted in accordance with the AIRR Data Representation schemas defined by the AIRR Community <http://docs.airr-community.org>.
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2025-04-22 |
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r-ampliconduo
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public |
Increasingly powerful techniques for high-throughput sequencing open the possibility to comprehensively characterize microbial communities, including rare species. However, a still unresolved issue are the substantial error rates in the experimental process generating these sequences. To overcome these limitations we propose an approach, where each sample is split and the same amplification and sequencing protocol is applied to both halves. This procedure should allow to detect likely PCR and sequencing artifacts, and true rare species by comparison of the results of both parts. The AmpliconDuo package, whereas amplicon duo from here on refers to the two amplicon data sets of a split sample, is intended to help interpret the obtained read frequency distribution across split samples, and to filter the false positive reads.
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2025-04-22 |
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r-aptreeshape
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public |
Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) <doi:10.1093/bioinformatics/bti798> and Maliet et al. (2017) <doi:10.1101/224295>.
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2025-04-22 |
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py2vega
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public |
A Python to Vega-expression transpiler.
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2025-04-22 |
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pyprojroot
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public |
Find project root paths and return relative project files
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2025-04-22 |
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hdf5-static
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public |
HDF5 is a data model, library, and file format for storing and managing data
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2025-04-22 |
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llvm-utils
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public |
Development headers and libraries for LLVM
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2025-04-22 |
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r-bedr
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public |
Genomic regions processing using open-source command line tools such as 'BEDTools', 'BEDOPS' and 'Tabix'. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. bedr API enhances access to these tools as well as offers additional utilities for genomic regions processing.
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2025-04-22 |
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r-funrar
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public |
Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
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2025-04-22 |
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r-rmcfs
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public |
MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M. Draminski, J. Koronacki (2018) <doi:10.18637/jss.v085.i12>.
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2025-04-22 |
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r-nam
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public |
Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
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2025-04-22 |
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r-enrichr
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public |
Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See (<http://amp.pharm.mssm.edu/Enrichr/>) for further details.
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2025-04-22 |
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r-loose.rock
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public |
Collection of functions to improve work-flow in survival analysis and data science. The package features include: the generation of balanced datasets, live retrieval of protein coding genes from two public databases, generation of random matrix based on covariance matrix, cache function to store function results. This work was supported by two grants from the Portuguese Foundation for Science and technology, and the EU Commission under SOUND project.
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2025-04-22 |
